Well, looking more in the deep, this seems more related to libSDL (that
is controlled by python-pygame).

Since one of the few things _WM atom parameters that libSDL sets is the
WM_CLASS, you can easily associate your application to a desktop file by
setting the environment variable (also inside the python script)
SDL_VIDEO_X11_WMCLASS to a value that can be the basename of your
.desktop file (i.e. if you run your python script with
SDL_VIDEO_X11_WMCLASS="gedit" python mygame.py it will be considered as
a gedit window, so just use your_deskto_basename and it will work).

However, I'm wondering how this could be improved directly in libSDL and/or 
pygame to make any pygame application work out of the box. Maybe the best 
solution would be making pygame always to export this environment variable (set 
to the program's basename) when running in X11.
If there aren't best suggestions, as soon as I can I will send a patch for 
implementing this in pygame.

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https://bugs.launchpad.net/bugs/777417

Title:
  Unity launcher doesn't work well with Python Pygame apps

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